Publications

Submitted / Preprints

35. Microscopic Phase-Field Modeling
    J. Jin^†, D. R. Reichman^†
    arXiv:2410.08180
36. Microscopic Theory of Density Scaling: Coarse-Graining in Space and Time
    J. Jin^†, D. R. Reichman^†, J. C. Dyre^†, U. R. Pedersen^†
    arXiv:2402.08675

Published

33. Systematic Bottom-Up Coarse-Graining of Hydrated Excess Proton Transport Across Scales
    J. Jin, Z. Li, G. A. Voth^†
    Nat. Comp. Sci. Accepted
34. Field-theoretic Simulation of Dean-Kawasaki Dynamics for Interacting Particles
    J. Jin^†, C. Liu, D. R. Reichman^†
    Phys. Rev. E., 2026, 113, 044138
35. A Bottom-Up Field-Theoretic Framework via Hierarchical Coarse-Graining: Generalized Mode Theory
    J. Jin*, Y. Han*, G. A. Voth^†
    J. Chem. Phys. 2026, 164, 084110
36. Bottom-Up Mesoscopic Coarse-Graining of Soft Matter
    J. Jin^†
    Nat. Rev. Phys. 2026, 8, 130
37. A benchmark of expert-level academic questions to assess AI capabilities
    L. Phan, ... , J. Jin, … , L. Schut
    Nature 2026, 649, 1139-1146
38. Understanding Dynamics in Coarse-Grained Models: V. Extension of Coarse-Grained Dynamics Theory to Non-Hard Sphere Systems
    J. Jin, G. A. Voth^†
    J. Chem. Phys. 2025, 162, 124114
39. A Tribute to Gregory A. Voth
    J. Jin^†, W. G. Noid^†, J. Li^†, R. Kumar^†, J. Cao^†, S. Jang^†, F. Paesani^†, D. Reichman^†
    J. Phys. Chem. B, 2024, 128, 7703-7706
40. Understanding Dynamics in Coarse-Grained Models: IV. Connection of Fine-Grained and Coarse-Grained Dynamics with the Stokes-Einstein and Stokes-Einstein-Debye Relations
    J. Jin, G. A. Voth^†
    J. Chem. Phys. 2024, 161, 034114
41. Hierarchical Framework for Predicting Entropies in Bottom-Up Coarse-Grained Models
    J. Jin^†, D. R. Reichman^†
    J. Phys. Chem. B, 2024, 128, 3182-3199 Selected as Front Cover
42. Perturbative Expansion in Reciprocal Space: Bridging Microscopic and Mesoscopic Descriptions of Molecular Interactions
    J. Jin^†, D. R. Reichman^†
    J. Phys. Chem. B, 2024, 128, 1061-1078
43. Gaussian Representation of Coarse-Grained Interactions of Liquids: Theory, Parametrization, and Transferability
    J. Jin, J. Hwang, G. A. Voth^†
    J. Chem. Phys. 2023, 159, 184105
44. Understanding Dynamics in Coarse-Grained Models: III. Roles of Rotational Motion and Translation-Rotation Coupling in Coarse-Grained Dynamics
    J. Jin, E. K. Lee, G. A. Voth^†
    J. Chem. Phys. 2023, 159, 164102
45. OpenMSCG: A Software Tool for Bottom-up Coarse-graining
    Y. Peng, A. J. Pak, A. E. P. Durumeric, P. G. Sahrmann, S. Mani, J. Jin, T. D. Loose, J. Beiter, G. A. Voth^†
    J. Phys. Chem. B 2023, 127, 8537-8550 Program WebsiteEditor’s Choice
46. Statistical Mechanical Design Principles for Coarse-Grained Interactions Across Different Conformational Free Energy Surfaces
    J. Jin, G. A. Voth^†
    J. Phys. Chem. Lett. 2023, 14, 1354-1362
47. Understanding Dynamics in Coarse-Grained Models: II. Coarse-Grained Diffusion Modeled Using Hard Sphere Theory
    J. Jin, K. S. Schweizer, G. A. Voth^†
    J. Chem. Phys. 2023, 158, 034104
48. Understanding Dynamics in Coarse-Grained Models: I. Universal Excess Entropy Scaling Relationship
    J. Jin, K. S. Schweizer, G. A. Voth^†
    J. Chem. Phys. 2023, 158, 034103 Featured
49. Bottom-Up Coarse-Graining: Principles and Perspectives
    J. Jin, A. J. Pak, A. E. P. Durumeric, T. D. Loose, G. A. Voth^†
    J. Chem. Theory Comput. 2022, 18, 5759-5791
50. Constructing Many-Body Dissipative Particle Dynamics Models of Fluids from Bottom-up Coarse-Graining
    Y. Han*, J. Jin*, G. A. Voth^†
    J. Chem. Phys. 2021, 154, 084122
51. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-Body Projected Water (BUMPer). II. Temperature Transferability and Structural Properties at Low Temperature
    J. Jin, A. J. Pak, Y. Han, G. A. Voth^†
    J. Chem. Phys. 2021, 154, 044105
52. A New One-Site Coarse-Grained Model for Water: Bottom-Up Many-Body Projected Water (BUMPer). I. General Theory and Model
    J. Jin, Y. Han, A. J. Pak, G. A. Voth^†
    J. Chem. Phys. 2021, 154, 044104 Editor’s Pick2021 JCP Editor's Choice
53. Temperature and Phase Transferable Bottom-up Coarse-Grained Models
    J. Jin, A. Yu, G. A. Voth^†
    J. Chem. Theory Comput. 2020, 16, 6823-6842
54. Atomic-scale Characterization of Mature HIV-1 Capsid Stabilization by Inositol Hexakisphosphate
    A. Yu, E. M. Lee, J. Jin, G. A. Voth^†
    Sci. Adv. 2020, 6, eabc6465 Featured in Phys.orgFeatured in UChicago News
55. Understanding missing entropy in coarse-grained systems: Addressing issues of representability and transferability
    J. Jin, A. J. Pak, G. A. Voth^†
    J. Phys. Chem. Lett. 2019, 10, 4549-4557
56. Coarse-Graining Involving Virtual Sites: Centers of Symmetry Coarse-Graining
    J. Jin*, Y. Han*, G. A. Voth^†
    J. Chem. Phys. 2019, 150, 154103
57. Coarse-Grained Simulations of Full-Length Integrin Activation
    T. C. Bidone, A. Polley*, J. Jin*, T. Driscoll, D. V. Iwamoto, D. A. Calderwood, M. A. Schwartz, G. A. Voth^†
    Biophys. J. 2019, 116, 1000-1010
58. Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding
    J. Jin, Y. Han, G. A. Voth^†
    J. Chem. Theory Comput. 2018, 14, 6159-6174
59. Ultra-Coarse-Grained Models Allow for an Accurate and Transferable Treatment of Interfacial Systems
    J. Jin, G. A. Voth^†
    J. Chem. Theory Comput. 2018, 14, 2180–2197 Special Virtual Issue
60. Correction to The Theory of Ultra-Coarse-Graining. 3. Coarse-grained Sites with Internal States in Rapid Local Equilibrium
    J. F. Dama*, J. Jin*, G. A. Voth^†
    J. Chem. Theory Comput. 2018, 14, 2288
61. Quantum Theory of Multiscale Coarse-Graining
    Y. Han, J. Jin, J. W. Wagner, G. A. Voth^†
    J. Chem. Phys. 2018, 148, 102335 Selected as Front CoverAIP Scilight InterviewFeatured
62. Extending the Range and Physical Accuracy of Coarse-Grained Models: Order Parameter Dependent Interactions
    J. W. Wagner, T. Dannenhoffer-Lafage, J. Jin, G. A. Voth^†
    J. Chem. Phys. 2017, 147, 044113
63. The Theory of Ultra-Coarse-Graining. 3. Coarse-Grained Sites with Internal States in Rapid Local Equilibrium
    J. F. Dama*, J. Jin*, G. A. Voth^†
    J. Chem. Theory Comput. 2017, 13, 1010–1022
64. Optical Nature and Binding Energetics of Fluorescent Fluoride Sensor Bis(bora)calix[4]arene and Design Strategies of its Homologues
    J. Jin, J. Y. Park, Y. S. Lee^†
    J. Phys. Chem. C 2016, 120, 24324–24334
65. Mechanisms Underlying the Mpemba Effect in Water from Molecular Dynamics Simulations
    J. Jin, W. A. Goddard III^†
    J. Phys. Chem. C 2015, 119, 2622–2629 Featured in Physics World